Technical Abstract:
The blast resistance (R) gene Pi-km protects rice against specific races of the fungal pathogen Magnaporthe oryzae. The use of blast R genes remains the most cost-effective method of disease control. To facilitate the breeding process, we developed a Pi-km specific molecular marker. For this purpose, we explored the existing sequence diversity for alleles of the two genes responsible for the Pi-km specificity in several U.S. rice cultivars. In 15 rice cultivars we found that the majority of nucleotide polymorphism was associated almost exclusively with the Pi-km1 allele. The amino acid variation was localized within the predicted coiled-coil domain of the Pi-km1 translated products. In contrast, the sequence of Pi-km2 alleles was highly conserved, even within cultivars more distantly related. Furthermore, the cultivars blast inoculation reaction patterns, as well as the two genes phylogenetic analysis, revealed a good correlation with known Pi-k genes (-k/ -kh/ -km/ -ks/ -kp) historically reported for some of these cultivars. Based on these findings, specific primer sets have been designed to discriminate among the various Pi-km sequence variants.